Streptococcus pneumoniae (S. pneumoniae) is a Gram-positive bacteria responsible for considerable morbidity and mortality (particularly in the young and aged), causing diseases such as pneumonia, bacteremia, meningitis, acute otitis media, and sinusitis. It is estimated the 20% of S. pneumoniae cases lead to bacteremia, and other manifestations such as meningitis, with a mortality rate close to 30% even with antibiotic treatment. S. pneumoniae is found in the nasopharynx of 11-76% of the population, averaging 40-50% for children and 20-30% for adults (Ghaffar et al., J. Infect. Dis. 18, 638-46, 1999).
Those most commonly at risk for pneumococcal infection are children between 6 months and 4 years of age and adults over 60 years of age. Virtually every child will experience pneumococcal otitis media before the age of 5 years. It is estimated that 25% of all community-acquired pneumonia is due to pneumococcus (1,000 per 100,000 inhabitants). Recently, epidemics of disease have reappeared in settings such as chronic care facilities, military camps, and day care centers, a situation not recognized since the pre-antibiotic era. S. pneumoniae remains a significant human pathogen because of the morbidity and mortality it causes in young children, the elderly and in immunocompromised patients.
The limitations of culture based, conventional S. pneumoniae diagnostic tests make definitive diagnosis difficult to establish. For example, the isolation of S. pneumoniae from blood, the recognized definitive test for the presence of S. pneumoniae may lack sensitive, only giving positive results in 20-30% of adult cases of pneumococcal pneumonia and less than 10% of children's cases. Serologic assays for both antibody and antigen detection suffer from a lack of specificity and sensitivity, for example the recently introduced urine antigen test, Binax NOW®, while shown to be sensitive and specific for adults by some studies, is unable to distinguish between carriage and disease in children.
In addition, the misidentification of pneumococcus-like viridans Streptococci (P-LVS) as S. pneumoniae presents additional opportunities for misdiagnosis especially when attempted with non-sterile site specimens such as sputum. Identification of S. pneumoniae has typically been based on bile solubility, optochin sensitivity, and GenProbe ACCUPROBE® Pneumococcus identification test; but increasingly there have been reports of P-LVS isolated from clinical specimens, which may give positive or variable reactions in one or more of these standard pneumococcal tests. Among a subset of reported isolates of P-LVS, a newly recognized species, classified as S. pseudopneumoniae (Spseudo), has been described and characterized (Arbique et al., J. Clin. Microbiol. 42: 4686-4696, 2004). Spseudo organisms are bile solubility negative and resistant to optochin in the presence of 5% CO2, but are ACCUPROBE® positive (Arbique et al., J. Clin. Microbiol. 42: 4686-4696, 2004) and thus yield a false positive for S. pneumoniae infection.
The appearance of these pneumococcus-like organisms has complicated identification and diagnosis even further, especially when non-sterile site respiratory specimens are used for making determinations. Therefore, special care must be taken to monitor and correctly identify confirmed pneumococci in the clinical setting. Thus, to make an accurate diagnosis the need exists for assays that can discriminate between S. pneumoniae and the Spseudo and other P-LVS species. The present disclosure meets this need by providing assays that can discriminate between S. pneumoniae and other organisms while still retaining high sensitivity for S. pneumoniae. 